David Jenkinson’s carbon studies opened the way for new research on soil biology

David Jenkinson, who has died aged 82, was an internationally respected soil scientist. His research was influential in setting patterns of thinking in diverse topics connected with soil, agriculture and the environment. These included the ways that agriculture influences climate change, how nitrogen fertiliser can be used more efficiently by farmers, and how microbes manage to survive in the inhospitable environment of soil.

David was born into an Irish family in Los Angeles. His family, affected by the stock market crash, returned to Northern Ireland when he was four and bought a farm in Armagh. He later said that watching the back-breaking labour involved in farming had made him keen that science should be used to ease it.

He attended the Royal school, Armagh, and won a scholarship to Trinity College Dublin, where he obtained a first in experimental science and did a PhD in organic chemistry. At university, he was involved in theatre and leftwing politics, and cultivated his lifelong enjoyment of the countryside.

His career in soil science research began in 1955 with an appointment at Reading University. In 1957 he moved to a research post at Rothamsted Experimental Station (now Rothamsted Research), the agricultural research centre at Harpenden, Hertfordshire, where he stayed until his retirement in 1988, although he remained scientifically active for at least a further 20 years. In 2010 he published a highly readable and authoritative online book, the title of which is typical of his style: Climate Change – A Brief Introduction for Scientists and Engineers – Or Anyone Else Who Has to Do Something About it.

In around 1960 he was among the first researchers to utilise the radioactive isotope carbon-14 to study the transformations of organic matter in soil. To achieve this, he grew plants in an atmosphere containing carbon dioxide "labelled" with carbon-14, using a special chamber that he designed and built himself. The plant material was then added to soil and its rate and pathway of decomposition followed. Using a radioactive "label" meant that the fate of the carbon from the freshly added material could be distinguished from carbon already in soil.

This led to several major developments, including a technique for measuring the quantity of carbon held in the cells of living microorganisms in soil. Treating soil microorganisms as a single entity (which he termed the "soil microbial biomass"), rather than using classical microbiological techniques to identify and count the different species, was a revolutionary step. It is analogous to studying an entire forest rather than individual trees.

David's 1966 publication on this topic opened the way for a new wave of research on soil biological processes, decades before the era of molecular biology. A much-cited paper published in 1976, co-written with David Powlson, built on this, and he went on to develop new concepts regarding the functioning and survival of microbes in soil, first in collaboration with Powlson and then with Phil Brookes.

David carried out pioneering work on the mathematical modelling of organic matter transformations in soil. He initially achieved this with James Rayner, and their efforts formed the basis of what is now the Rothamsted carbon model, RothC. This is widely used today, both in research and in schemes to quantify soil carbon stocks as part of emerging carbon accreditation schemes. David published an updated version of the model three years ago.

He was among the first to recognise the significance of the world's soil carbon stocks in the context of climate change – either making things worse, through the additional release of carbon dioxide as the world warms, or better, by locking up additional carbon through careful land management. His paper in Nature in 1991 was the first quantitative assessment of the potential for a "feedback effect" in which the additional carbon dioxide released from decomposition of organic matter in soil in a warmer world accelerates climate change still further.

During the 1980s he turned his attention to the nitrogen cycle by initiating a programme of research on the efficiency with which nitrogen fertiliser is used by crops, utilising the stable isotope of nitrogen, nitrogen-15, in field experiments. This work led to much of our current thinking on the role of nitrogen fertiliser as a key contributor to achieving global food security. It also laid foundations for understanding the environmental impacts of poor utilisation of nitrogen. David combined results from this phase of his career with his carbon modelling studies to build a model of nitrogen transformations, designed to help farmers calculate appropriate applications of fertilisers.

David was elected a fellow of the Royal Society in 1991. He received the Massey Ferguson national agricultural award in 1993 and was elected an honorary member of the Soil Science Society of America (1995) and the British Society of Soil Science (2007). After his retirement he was appointed a Lawes Trust senior fellow at Rothamsted, and a visiting professor at Reading University.

He is survived by his wife, Moira, and his children, Hugh, Philip, Maeve and Robert.

• David Jenkinson, soil scientist, born 25 February 1928; died 16 February 2011